ecotype: Col-0 genotype: wildtype age: 17 days tissue: whole plant
Extracted molecule
total RNA
Extraction protocol
Qiagen RNAeasy kit protocol
Label
biotin
Label protocol
Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling
Hybridization protocol
Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA
Scan protocol
Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.
Description
Before sowing, seeds were placed at 4°C for 3 days Arabidopsis seedlings were grown in growth chambers at 22°C supplied with continuous light. Before sowing, seeds were placed at 4°C for 3 days for stratification. Individual seeds were planted on pre-wetted pots of 2 sq inches containing a mixture of 3:1 compost and sand previously treated with the insecticide Intercept. Pots were placed in trays and covered with propagators, which were removed 8 days after seed germination. Seedlings were watered regularly until the tissue was collected for RNA extraction. Growth chamber Commercial soil 65 21
Data processing
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system
